[gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)

Marc Hömberger hoembi at gmail.com
Wed May 30 13:47:30 CEST 2012


when I try the mentioned method for the GROMACs output (xvg file,
supposedly formatted for use with xmgrace) I am unable to print the
standarddeviation. I f I select the XYDY method it just ignores it and
plots again an XY graph.

What I then did: I stripped the file so that only residue number (column
1), average (column 2) and the standarddeviation (column 3) are in the file
(each comma seperated by a single space). When i open that in xmgrace and I
select the XYDY set it is displayed correctly.
However, this means I have to strip each file. Is there any way I can
circumvent stripping every single file?


On Wed, May 30, 2012 at 6:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> On 5/30/12 4:58 AM, Marc Hömberger wrote:
>> Hello,
>> I am currently analyzing a bunch of trajectories and one thing I am doing
>> is to
>> use g_sas to generate the average and standard deviation per residue. The
>> resulting xvg file should be formatted for use with xmgrace but I do not
>> seem to
>> be able to get the standard deviation in the graph. I tried searching for
>> some
>> hints and also looked through xmgrace's manual but there was nothing
>> about file
>> format where the second column is the standardeviation and how to show
>> that in
>> the graph. Can anyone of you maybe point me in the right direction on how
>> to
>> plot the averages plus the corresponding standard deviation?
> In the window for importing data, choose "XYDY" from the "Set type"
> dropdown menu.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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